Liatris Update

Good news on the Liatris front: all hands-on work, from harvesting to x-raying, is complete! The process began in the summer of 2021 and involved lots of help from the field crew, wise, long-term Team Echinacea members, eager and efficient short-term members, and everyone in between.

Mia V and I were also able to complete data entry and data cleaning today, paving the road forward for analysis.

Now that we’re moving on to computer work, we came up with some primary questions to pursue (and some hypotheses):

  • Is there a significant difference in seed predation rates between burned and unburned and unburned remnants?
    • We suspect that predation will be higher in burned remnants because density of plants will be higher
  • Is there a correlation between seed predation rates and plant density?
    • We hypothesize that higher density will be correlated with higher rates of predation
    • We will use nearest neighbor as our measure of density
  • Is there a correlation between individual plant size and predation rates?
    • We hypothesize that larger plants will receive higher rates of predation
    • We will use number of flowering heads as our measure of plant size.

I’m now in the process of making plots to help us visualize the data we’ve collected, and soon we can begin to seek answers for our questions.

Because none of our questions at the moment directly relate to pollination, we don’t need to quantify seed set, which is the “classify” step. Using the x-rays to count how many achenes contain seeds is our method of determining pollination rates (seed = pollinated, no seed = not pollinated). This step will likely stay low priority for awhile, so don’t fret about the empty bar. All part of the plan.


Liatris Update

Liatris aspera 2021 progress in the lab is steadily marching on. Thanks to the work of the Carleton externs last winter, we began Northwestern’s spring quarter essentially halfway done (only needing to do some brief back-peddling due to a change in protocol).

With the help of work study Mia V., cleaning, the process of removing the achenes from the flowering heads and gather data on achene-per-head count, is completely finished. Mia has also made excellent progress on randomizing, the step where we select a random sample of achenes to be x-rayed as well as quantify seed predation. We’re on track to finish randomizing later this week or next. Following that, we can x-ray the final batch of 56 liatris, allowing us to quantify seed set, and all the hands-on work for our 234 liatris from 2021 will be complete!

Priorities going forward:

  • Finish randomizing and x-raying for batch D
  • Complete randomization data entry and verification
  • Develop methods of data analysis to compare
    • Burned vs. unburned predation rates
      • In regards to density
      • In regards to number of heads per plant
  • Develop methods of classifying seed set from x-rays (low priority)

burning androPilot (east) 2022

To kick off our 2022 burn season, we conducted a prescribed burn in our eastern pilot Andropogon experimental plot on Friday, May 6. We burned the western plot in spring 2021.

After staging equipment and checking the weather with our new bluetooth-enabled Kestrel, we ignited a test fire in the NW corner of the plot. The fire looked great and out mowed break was doing its job so we proceeded with the fire. Stuart kept watch over the northern line while Alex and Trygg tended to the western edge. We allowed the fire to back downhill against the wind. After putting in a few strips to quickly widen the black, we ignited along the eastern and southern lines. The headfire quickly ran uphill. Apart from areas with discontinuous fuels along the northern edge, the burn was pretty thorough. Stuart noted that the wind was consistently southeast except for a southern push when we ignited the headfire. We agreed that lighting the headfire sooner would have been possible given conditions and the fire behavior we observed. All-in-all, a successful first burn of 2022 for the Echinacea Project. We are eager to learn how Andropogon gerardii responds to fire.

Temperature: 65 F
Relative Humidity: 37 %
Wind Speed: 13 mph
Wind Direction: SE
Ignition time: 12:03 PM
End time: 12:24 PM
Burn Crew: Jared, Stuart, Alex C., Trygg

Lilium Project Update

         The lilium project is almost wrapping up as I am approaching the end of my semester long internship. I am almost finished with processing my seed data. All the scans and x-rays of lilium ovules have been done. The only steps left are to finish counting and classifying the ovules. Counting is done to quantify the total number of ovules in the each lilium pod. Classifying is using the x-ray image to determine the number of fertilized ovules in each pod. Once I have the data for the total and full counts of each lilium pod, I will be able to obtain the seed set for each individual lilium philadelphicum. Then, I will analyze the relationship between variation in seed set and proximity in nearest neighboring plants. Jared showed me the FNN package in R which, like its name, will find the nearest neighbor between x and y coordinates. The knn.dist function is a handy tool that allows you to compare distances of a point and its nth neighbors. In order to further analyze the data, my first step is to conduct data management and organize the different variables into a data frame. This process is very useful for researchers that use R for data analysis and data visualization. Next week, I will have a data frame that includes the information necessary for the analysis and visualization of the lilium data. 

Staffanson demap update

For the remnants, I finished data reconciliation for all the plants at Staffanson Prairie Preserve (spp) through 2021 in demap, our repository for data from the remnants. Each summer, we use the GPS to record the positions of every flowering Echinacea angustifolia plant within the transect at Staffanson, and we also revisit plants that flowered previously to check whether they are still alive, a process called total demo. This winter, I connected records between years so we can track the life of individual plants across the years.

Last week, I completed demo.out for Staffanson in 2017, 2018, 2019, 2020, and 2021. Demo.out makes one record for each plant that we visited each year and records whether it was living or dead, whether it flowered, and how many heads it had. This is the dataset that we can use to do longitudinal data analysis and study the demography of Echinacea plants over time. In 2020, both sides of Staffanson burned, and it had the highest flowering rate in the past 5 years – 275 plants! Of those plants, 33 flowered for the first time. In 2021, there was just one new flowering plant.

E. pallida & hybrid heads 2020

A note to future Team Echinacea members: Are you still wearing masks all the time? Are you still 3 years behind on cleaning Echinacea heads or have you caught up a little bit?

Anyway, in the summer of 2020 there were 18 heads of Echinacea pallida that were harvested. 11 of these heads were a part of Anna Meehan’s hybrid compatibility experiment. All of the pallida heads are NOT going through the ACE process; they are in the lab all together nice and neat. These 18 pallida heads will not be a part of hh2020. EXCEPT the hybrid plant head (AP-772) who will stay apart of hh.2020 since we need achene count eventually but for now it will stay here until it is dissected.

The heads are in a box labeled “Anna Meehan’s Hybrid Compatibility experiment & E. pallida heads 2020″ in the glass cabinets right as you enter the ecology lab.

The hybrid compatibility experiment would be a perfect project for a student in the lab for a few weeks. They could asses the compatibility of the hybrid with not only the E. angustifolia but also the E. pallida. The experiment is designed with backcrosses (hybrid to parent) and forward crosses (parent to hybrid don’t know if this is the right word I just made it up). The student would be able to access seed set on the hybrid, E. angustifolia, & E. pallida heads. The sample size is fairly small but this would conclude a good pilot study for further studies of the hybrid compatibilities. We also need achene count of the hybrid plant (AP-227)!

Aphids at MEEC

On March 5, 2022, Allie and Wyatt presented about aphids and prescribed fire at the Midwest Ecology and Evolution Conference (MEEC). See the poster below!

Roadside pollinators at MEEC

On March 5, 2022, Mia and Alex presented the Pollinators on Roadsides project at the Midwest Ecology and Evolution Conference (MEEC). They focused on the bee abundance results since the specimens had not been fully identified to species yet.

Amy visits CBG!

On Friday, grad student Amy W. paid a visit to the lab at the Chicago Botanic Garden to x-ray Echinacea achenes for several of her projects including the Dust Project, interremnant crosses, and gene flow experiments. We’re thrilled to have a functional x-ray machine once again. Amy noticed lots of variation in her samples, so we’re excited to learn about seed set for these experiments!

Week 7: X-ray Time

This week I continued to make progress on cleaning and scanning for the lilium project (Figure 2). All the pods have been cleaned and we have established a scanning protocol for lilium pods. These protocols allow for others to replicate our methods in future projects with lilies.

Jared and I conducted a couple trials with x-raying the lilium seeds. We will experiment with adjusting the settings on the x-ray and after effects for the images. Further experimentation is necessary to generate high quality x-ray scans in order to classify the seeds. In the x-ray images, the seeds that contain fertilized embryos will appear bright white (Figure 1). We use this to classify which seeds contain fertilized embryos and which ones are empty. The contrast of appearance in the x-ray is due to the increase in density of the fertilized embryos.